Casal2 Test Case MPD comparisons for LIN

1 LIN comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-6 vs. 2e-3).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3).

1.1 LIN model characteristics

The main characteristics of the Test Case LIN (ling) CASAL model are:

• one stock, ages 3 - 25
• one area
• years 1972 - 2018, projection years 2019 - 2023
• two time steps: Dec_Aug and Sep_Nov
• two stock categories: male and female
• natural mortality-at-age is double exponential
• sex-specific maturity ogives specified by age
• sex-specific von Bertalanffy age-length relationship
• sex-specific length-weight relationship (\(W = aL^b\))
• Beverton-Holt stock-recruitment relationship, with steepness (h) 0.84
• ageing error
• two surveys with sex-specific logistic selectivity
• three fisheries, one with double normal selectivity and two with logistic selectivity

Observation data include:

• survey indices
• survey proportions-at-age
• fishery proportions-at-age

Parameters estimated include:

• B0
• parameters for the natural mortality-at-age ogive
• catchability (q) for the two surveys
• parameters for the sex-specific selectivity curves for the two surveys
• parameters for the sex-specific selectivity curves for the three fisheries
• YCS (recruitment deviations)

1.2 R environment

## [1] "Tue Sep 14 11:23:56 2021"
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 11 (bullseye)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Casal2_21.08   casal_2.30     devtools_2.4.2 usethis_2.0.1  rlist_0.4.6.2 
##  [6] ggthemes_4.2.4 gridExtra_2.3  coda_0.19-4    ggmcmc_1.5.1.1 ggplot2_3.3.5 
## [11] tidyr_1.1.3    dplyr_1.0.7   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7         lattice_0.20-41    prettyunits_1.1.1  ps_1.6.0          
##  [5] assertthat_0.2.1   rprojroot_2.0.2    digest_0.6.27      utf8_1.2.2        
##  [9] R6_2.5.1           plyr_1.8.6         evaluate_0.14      pillar_1.6.2      
## [13] rlang_0.4.11       rstudioapi_0.13    data.table_1.14.0  callr_3.7.0       
## [17] jquerylib_0.1.4    rmarkdown_2.10     desc_1.3.0         stringr_1.4.0     
## [21] munsell_0.5.0      compiler_3.6.3     xfun_0.25          pkgconfig_2.0.3   
## [25] pkgbuild_1.2.0     htmltools_0.5.2    tidyselect_1.1.1   tibble_3.1.4      
## [29] reshape_0.8.8      fansi_0.5.0        crayon_1.4.1       withr_2.4.2       
## [33] grid_3.6.3         jsonlite_1.7.2     GGally_2.1.2       gtable_0.3.0      
## [37] lifecycle_1.0.0    DBI_1.1.1          magrittr_2.0.1     scales_1.1.1      
## [41] cli_3.0.1          stringi_1.7.4      cachem_1.0.6       remotes_2.4.0     
## [45] fs_1.5.0           testthat_3.0.4     bslib_0.3.0        ellipsis_0.3.2    
## [49] generics_0.1.0     vctrs_0.3.8        RColorBrewer_1.1-2 tools_3.6.3       
## [53] glue_1.4.2         purrr_0.3.4        processx_3.5.2     pkgload_1.2.2     
## [57] fastmap_1.1.0      yaml_2.2.1         colorspace_2.0-2   sessioninfo_1.1.1 
## [61] memoise_2.0.0      knitr_1.34         sass_0.4.0

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')

source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates

rownames	Base_Model	Sensitivity_1	Percent_Diff
q[tan_sum].q	0.09128	0.09105	0.252
q[tan_aut].q	0.12620	0.12590	0.238
initialization.B0	309000.00000	310700.00000	-0.550
natural_mortality.ogive_all1	12.49000	12.98000	-3.923
natural_mortality.ogive_all2	0.13270	0.12780	3.693
natural_mortality.ogive_all3	0.38190	0.44990	-17.806
natural_mortality.ogive_all4	0.35060	0.35390	-0.941
selectivity[surveysum_sel].male1	4.73800	4.88100	-3.018
selectivity[surveysum_sel].male2	1.75000	1.77200	-1.257
selectivity[surveysum_sel].male3	0.61000	0.60160	1.377
selectivity[surveysum_sel].female1	5.46000	5.61300	-2.802
selectivity[surveysum_sel].female2	2.20600	2.21500	-0.408
selectivity[surveyaut_sel].male1	5.50400	5.64400	-2.544
selectivity[surveyaut_sel].male2	2.31400	2.29800	0.691
selectivity[surveyaut_sel].male3	0.93920	0.93310	0.649
selectivity[surveyaut_sel].female1	5.92000	6.06200	-2.399
selectivity[surveyaut_sel].female2	2.77800	2.73800	1.440
selectivity[trawl_sel].male1	8.37000	8.40400	-0.406
selectivity[trawl_sel].male2	1.97200	1.94700	1.268
selectivity[trawl_sel].male3	61.65000	200.00000	-224.412
selectivity[trawl_sel].male4	1.04100	1.02100	1.921
selectivity[trawl_sel].female1	8.66400	8.74100	-0.889
selectivity[trawl_sel].female2	2.10000	2.08800	0.571
selectivity[trawl_sel].female3	43.31000	40.38000	6.765
selectivity[line_home_sel].male1	11.45000	8.58300	25.039
selectivity[line_home_sel].male2	8.59000	4.54700	47.066
selectivity[line_home_sel].male3	0.38010	0.26910	29.203
selectivity[line_home_sel].female1	9.61600	9.53100	0.884
selectivity[line_home_sel].female2	3.87500	3.68500	4.903
selectivity[line_spawn_sel].male1	18.30000	14.04000	23.279
selectivity[line_spawn_sel].male2	13.67000	10.01000	26.774
selectivity[line_spawn_sel].male3	1.86800	1.17300	37.206
selectivity[line_spawn_sel].female1	9.74600	9.71300	0.339
selectivity[line_spawn_sel].female2	3.00800	2.89400	3.790
recruitment.YCS1	1.00000	1.00000	0.000
recruitment.YCS2	1.00000	1.00000	0.000
recruitment.YCS3	1.00000	1.00000	0.000
recruitment.YCS4	1.00000	1.00000	0.000
recruitment.YCS5	0.48500	0.46620	3.876
recruitment.YCS6	0.45830	0.45010	1.789
recruitment.YCS7	0.56860	0.56470	0.686
recruitment.YCS8	0.56670	0.56670	0.000
recruitment.YCS9	0.48610	0.49070	-0.946
recruitment.YCS10	0.55500	0.56720	-2.198
recruitment.YCS11	0.56320	0.57880	-2.770
recruitment.YCS12	0.68760	0.71090	-3.389
recruitment.YCS13	0.62030	0.63610	-2.547
recruitment.YCS14	0.79060	0.80840	-2.251
recruitment.YCS15	0.46430	0.46930	-1.077
recruitment.YCS16	0.70080	0.70730	-0.928
recruitment.YCS17	0.41010	0.41050	-0.098
recruitment.YCS18	0.51500	0.51450	0.097
recruitment.YCS19	0.34160	0.34220	-0.176
recruitment.YCS20	0.34830	0.34730	0.287
recruitment.YCS21	0.43610	0.43820	-0.482
recruitment.YCS22	0.48060	0.47500	1.165
recruitment.YCS23	0.45220	0.45130	0.199
recruitment.YCS24	0.49170	0.49480	-0.630
recruitment.YCS25	0.46910	0.47070	-0.341
recruitment.YCS26	0.79930	0.80490	-0.701
recruitment.YCS27	0.79010	0.79210	-0.253
recruitment.YCS28	0.82610	0.83110	-0.605
recruitment.YCS29	0.70760	0.71250	-0.692
recruitment.YCS30	0.55170	0.55430	-0.471
recruitment.YCS31	0.47520	0.47680	-0.337
recruitment.YCS32	0.46170	0.46140	0.065
recruitment.YCS33	0.55500	0.55430	0.126
recruitment.YCS34	0.54670	0.54210	0.841
recruitment.YCS35	0.48320	0.48250	0.145
recruitment.YCS36	0.55020	0.54990	0.055
recruitment.YCS37	0.61530	0.61580	-0.081
recruitment.YCS38	0.77570	0.77470	0.129
recruitment.YCS39	0.63110	0.63060	0.079
recruitment.YCS40	0.77550	0.77350	0.258
recruitment.YCS41	0.64290	0.63930	0.560
recruitment.YCS42	0.70670	0.69940	1.033
recruitment.YCS43	0.65430	0.64860	0.871
recruitment.YCS44	0.51000	0.50620	0.745
recruitment.YCS45	0.58620	0.58730	-0.188
recruitment.YCS46	0.60350	0.58930	2.353
recruitment.YCS47	0.57680	0.57450	0.399

Casal2 parameter estimates

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	308529.00000	308529.00000	310577.00000	266100.00000	266100.00000	292654.00000
catchability[summerTANq].q	0.09137	0.09137	0.09106	0.10650	0.10650	0.09747
catchability[autumnTANq].q	0.12607	0.12607	0.12594	0.14712	0.14712	0.13444
selectivity[M_all].x0	12.49650	12.49650	12.98440	14.44070	14.44070	13.00000
selectivity[M_all].y0	0.13262	0.13262	0.12797	0.12992	0.12992	0.12855
selectivity[M_all].y1	0.38280	0.38280	0.44726	0.28861	0.28861	0.35795
selectivity[M_all].y2	0.35113	0.35113	0.35373	0.39560	0.39560	0.36956
selectivity[summerTANSel_m].a50	4.73988	4.73988	4.87645	4.57732	4.57732	4.69873
selectivity[summerTANSel_m].ato95	1.74459	1.74459	1.77029	1.73764	1.73764	1.74362
selectivity[summerTANSel_m].alpha	0.60995	0.60995	0.60184	0.61814	0.61814	0.61059
selectivity[summerTANSel_f].a50	5.46111	5.46111	5.60807	5.28798	5.28798	5.42487
selectivity[summerTANSel_f].ato95	2.20340	2.20340	2.21420	2.19028	2.19028	2.21398
selectivity[autumnTANSel_m].a50	5.50982	5.50982	5.63972	5.73059	5.73059	5.49015
selectivity[autumnTANSel_m].ato95	2.31271	2.31271	2.29781	2.99008	2.99008	2.34468
selectivity[autumnTANSel_m].alpha	0.94173	0.94173	0.93320	0.96024	0.96024	0.93567
selectivity[autumnTANSel_f].a50	5.91574	5.91574	6.05848	5.92344	5.92344	5.91564
selectivity[autumnTANSel_f].ato95	2.77020	2.77020	2.73846	3.02529	3.02529	2.83473
selectivity[trwlFSel_m].mu	8.36919	8.36919	8.40239	8.04058	8.04058	8.31968
selectivity[trwlFSel_m].sigma_l	1.97023	1.97023	1.94735	1.83023	1.83023	1.96278
selectivity[trwlFSel_m].sigma_r	61.52290	61.52290	200.00000	173.12600	173.12600	195.82200
selectivity[trwlFSel_m].alpha	1.04276	1.04276	1.02085	1.03254	1.03254	1.03107
selectivity[trwlFSel_f].mu	8.65854	8.65854	8.73949	8.44894	8.44895	8.64021
selectivity[trwlFSel_f].sigma_l	2.09656	2.09656	2.08849	2.02288	2.02288	2.10291
selectivity[trwlFSel_f].sigma_r	43.16390	43.16390	40.59470	74.44980	74.44950	196.08500
selectivity[lineHomeFSel_m].a50	11.45600	11.45600	8.60835	11.14980	11.14970	10.33100
selectivity[lineHomeFSel_m].ato95	8.59958	8.59958	4.59169	8.60490	8.60487	7.36215
selectivity[lineHomeFSel_m].alpha	0.38022	0.38022	0.26993	0.36159	0.36159	0.33090
selectivity[lineHomeFSel_f].a50	9.61476	9.61476	9.53352	9.65872	9.65871	9.61305
selectivity[lineHomeFSel_f].ato95	3.87014	3.87014	3.69064	3.95871	3.95871	3.89494
selectivity[lineSpawnFSel_m].a50	18.21510	18.21510	14.04670	28.70470	28.70470	29.95770
selectivity[lineSpawnFSel_m].ato95	13.59950	13.59950	10.02610	19.71220	19.71220	20.36400
selectivity[lineSpawnFSel_m].alpha	1.85634	1.85634	1.17449	4.70245	4.70245	4.98330
selectivity[lineSpawnFSel_f].a50	9.73862	9.73862	9.71478	9.73149	9.73149	9.82125
selectivity[lineSpawnFSel_f].ato95	2.99387	2.99387	2.89670	2.94900	2.94900	3.10917
process[Recruitment].ycs_values{1972}	0.48379	0.48379	0.46642	0.96089	0.96089	0.47028
process[Recruitment].ycs_values{1973}	0.46122	0.46122	0.45020	0.17029	0.17029	0.44943
process[Recruitment].ycs_values{1974}	0.56837	0.56837	0.56454	1.33842	1.33843	0.55135
process[Recruitment].ycs_values{1975}	0.56652	0.56652	0.56688	1.06126	1.06126	0.56278
process[Recruitment].ycs_values{1976}	0.48635	0.48635	0.49081	0.65452	0.65452	0.47857
process[Recruitment].ycs_values{1977}	0.55413	0.55413	0.56717	1.11613	1.11613	0.55411
process[Recruitment].ycs_values{1978}	0.56316	0.56316	0.57855	0.87968	0.87968	0.56121
process[Recruitment].ycs_values{1979}	0.68899	0.68899	0.71094	1.25909	1.25909	0.69474
process[Recruitment].ycs_values{1980}	0.62093	0.62093	0.63619	0.97826	0.97826	0.62242
process[Recruitment].ycs_values{1981}	0.79247	0.79247	0.80802	1.39968	1.39968	0.79761
process[Recruitment].ycs_values{1982}	0.46507	0.46507	0.46928	0.81405	0.81405	0.46578
process[Recruitment].ycs_values{1983}	0.69967	0.69967	0.70706	1.21889	1.21889	0.70914
process[Recruitment].ycs_values{1984}	0.40995	0.40995	0.41042	0.67843	0.67843	0.41357
process[Recruitment].ycs_values{1985}	0.51540	0.51540	0.51456	0.89968	0.89968	0.52216
process[Recruitment].ycs_values{1986}	0.34131	0.34131	0.34212	0.63379	0.63379	0.34658
process[Recruitment].ycs_values{1987}	0.34760	0.34760	0.34728	0.63848	0.63848	0.35081
process[Recruitment].ycs_values{1988}	0.43791	0.43791	0.43826	0.69906	0.69906	0.44356
process[Recruitment].ycs_values{1989}	0.47924	0.47924	0.47500	0.84529	0.84529	0.48296
process[Recruitment].ycs_values{1990}	0.45181	0.45181	0.45133	0.83046	0.83046	0.45748
process[Recruitment].ycs_values{1991}	0.49264	0.49264	0.49479	0.83278	0.83278	0.49530
process[Recruitment].ycs_values{1992}	0.46918	0.46918	0.47070	0.84190	0.84190	0.47280
process[Recruitment].ycs_values{1993}	0.79791	0.79791	0.80486	1.37198	1.37198	0.79546
process[Recruitment].ycs_values{1994}	0.79128	0.79128	0.79208	1.36560	1.36560	0.79353
process[Recruitment].ycs_values{1995}	0.82538	0.82538	0.83109	1.33636	1.33636	0.82230
process[Recruitment].ycs_values{1996}	0.70728	0.70728	0.71248	1.17799	1.17799	0.70676
process[Recruitment].ycs_values{1997}	0.55206	0.55206	0.55427	0.92843	0.92843	0.54976
process[Recruitment].ycs_values{1998}	0.47508	0.47508	0.47683	0.81100	0.81100	0.47576
process[Recruitment].ycs_values{1999}	0.46119	0.46119	0.46140	0.81281	0.81281	0.45950
process[Recruitment].ycs_values{2000}	0.55575	0.55575	0.55442	0.90770	0.90770	0.55642
process[Recruitment].ycs_values{2001}	0.54546	0.54546	0.54206	0.89998	0.89998	0.54587
process[Recruitment].ycs_values{2002}	0.48373	0.48373	0.48263	0.83336	0.83336	0.48578
process[Recruitment].ycs_values{2003}	0.54989	0.54989	0.54993	0.90389	0.90389	0.55113
process[Recruitment].ycs_values{2004}	0.61418	0.61418	0.61578	1.02665	1.02665	0.62023
process[Recruitment].ycs_values{2005}	0.77712	0.77712	0.77462	1.26528	1.26528	0.78192
process[Recruitment].ycs_values{2006}	0.63130	0.63130	0.63052	1.06897	1.06897	0.63677
process[Recruitment].ycs_values{2007}	0.77377	0.77377	0.77345	1.19541	1.19541	0.77965
process[Recruitment].ycs_values{2008}	0.64251	0.64251	0.63928	1.03558	1.03558	0.64725
process[Recruitment].ycs_values{2009}	0.70649	0.70649	0.69935	1.05005	1.05005	0.70700
process[Recruitment].ycs_values{2010}	0.65312	0.65312	0.64871	0.98732	0.98732	0.65008
process[Recruitment].ycs_values{2011}	0.51136	0.51136	0.50623	0.91803	0.91803	0.51091
process[Recruitment].ycs_values{2012}	0.58556	0.58556	0.58738	0.95384	0.95384	0.58606
process[Recruitment].ycs_values{2013}	0.60064	0.60064	0.58912	0.96522	0.96522	0.60398
process[Recruitment].ycs_values{2014}	0.57601	0.57601	0.57450	0.96646	0.96646	0.57961

Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	0.000	0.000	-0.664	13.752	13.752	5.145
catchability[summerTANq].q	0.000	0.000	0.344	-16.560	-16.560	-6.675
catchability[autumnTANq].q	0.000	0.000	0.105	-16.694	-16.694	-6.634
selectivity[M_all].x0	0.000	0.000	-3.904	-15.558	-15.558	-4.029
selectivity[M_all].y0	0.000	0.000	3.510	2.041	2.041	3.071
selectivity[M_all].y1	0.000	0.000	-16.840	24.606	24.606	6.491
selectivity[M_all].y2	0.000	0.000	-0.741	-12.665	-12.665	-5.249
selectivity[summerTANSel_m].a50	0.000	0.000	-2.881	3.430	3.430	0.868
selectivity[summerTANSel_m].ato95	0.000	0.000	-1.473	0.398	0.398	0.056
selectivity[summerTANSel_m].alpha	0.000	0.000	1.329	-1.344	-1.344	-0.106
selectivity[summerTANSel_f].a50	0.000	0.000	-2.691	3.170	3.170	0.664
selectivity[summerTANSel_f].ato95	0.000	0.000	-0.490	0.595	0.595	-0.480
selectivity[autumnTANSel_m].a50	0.000	0.000	-2.358	-4.007	-4.007	0.357
selectivity[autumnTANSel_m].ato95	0.000	0.000	0.644	-29.289	-29.289	-1.382
selectivity[autumnTANSel_m].alpha	0.000	0.000	0.906	-1.965	-1.965	0.644
selectivity[autumnTANSel_f].a50	0.000	0.000	-2.413	-0.130	-0.130	0.002
selectivity[autumnTANSel_f].ato95	0.000	0.000	1.146	-9.208	-9.208	-2.329
selectivity[trwlFSel_m].mu	0.000	0.000	-0.397	3.926	3.926	0.592
selectivity[trwlFSel_m].sigma_l	0.000	0.000	1.161	7.106	7.106	0.378
selectivity[trwlFSel_m].sigma_r	0.000	0.000	-225.082	-181.401	-181.401	-218.291
selectivity[trwlFSel_m].alpha	0.000	0.000	2.101	0.980	0.980	1.121
selectivity[trwlFSel_f].mu	0.000	0.000	-0.935	2.421	2.421	0.212
selectivity[trwlFSel_f].sigma_l	0.000	0.000	0.385	3.514	3.514	-0.303
selectivity[trwlFSel_f].sigma_r	0.000	0.000	5.952	-72.482	-72.481	-354.280
selectivity[lineHomeFSel_m].a50	0.000	0.000	24.857	2.673	2.674	9.820
selectivity[lineHomeFSel_m].ato95	0.000	0.000	46.606	-0.062	-0.062	14.389
selectivity[lineHomeFSel_m].alpha	0.000	0.000	29.007	4.900	4.900	12.971
selectivity[lineHomeFSel_f].a50	0.000	0.000	0.845	-0.457	-0.457	0.018
selectivity[lineHomeFSel_f].ato95	0.000	0.000	4.638	-2.289	-2.289	-0.641
selectivity[lineSpawnFSel_m].a50	0.000	0.000	22.884	-57.587	-57.587	-64.466
selectivity[lineSpawnFSel_m].ato95	0.000	0.000	26.276	-44.948	-44.948	-49.741
selectivity[lineSpawnFSel_m].alpha	0.000	0.000	36.731	-153.318	-153.318	-168.448
selectivity[lineSpawnFSel_f].a50	0.000	0.000	0.245	0.073	0.073	-0.848
selectivity[lineSpawnFSel_f].ato95	0.000	0.000	3.246	1.499	1.499	-3.851
process[Recruitment].ycs_values{1972}	0.000	0.000	3.589	-98.618	-98.618	2.792
process[Recruitment].ycs_values{1973}	0.000	0.000	2.389	63.078	63.078	2.557
process[Recruitment].ycs_values{1974}	0.000	0.000	0.675	-135.483	-135.485	2.995
process[Recruitment].ycs_values{1975}	0.000	0.000	-0.064	-87.331	-87.331	0.659
process[Recruitment].ycs_values{1976}	0.000	0.000	-0.916	-34.578	-34.578	1.599
process[Recruitment].ycs_values{1977}	0.000	0.000	-2.353	-101.420	-101.420	0.004
process[Recruitment].ycs_values{1978}	0.000	0.000	-2.733	-56.206	-56.206	0.346
process[Recruitment].ycs_values{1979}	0.000	0.000	-3.185	-82.743	-82.743	-0.835
process[Recruitment].ycs_values{1980}	0.000	0.000	-2.457	-57.547	-57.547	-0.239
process[Recruitment].ycs_values{1981}	0.000	0.000	-1.962	-76.622	-76.622	-0.649
process[Recruitment].ycs_values{1982}	0.000	0.000	-0.906	-75.037	-75.038	-0.152
process[Recruitment].ycs_values{1983}	0.000	0.000	-1.056	-74.210	-74.210	-1.353
process[Recruitment].ycs_values{1984}	0.000	0.000	-0.115	-65.490	-65.490	-0.883
process[Recruitment].ycs_values{1985}	0.000	0.000	0.162	-74.561	-74.561	-1.313
process[Recruitment].ycs_values{1986}	0.000	0.000	-0.236	-85.692	-85.692	-1.545
process[Recruitment].ycs_values{1987}	0.000	0.000	0.091	-83.683	-83.683	-0.925
process[Recruitment].ycs_values{1988}	0.000	0.000	-0.079	-59.635	-59.635	-1.290
process[Recruitment].ycs_values{1989}	0.000	0.000	0.884	-76.381	-76.381	-0.775
process[Recruitment].ycs_values{1990}	0.000	0.000	0.106	-83.808	-83.808	-1.256
process[Recruitment].ycs_values{1991}	0.000	0.000	-0.436	-69.043	-69.043	-0.539
process[Recruitment].ycs_values{1992}	0.000	0.000	-0.325	-79.442	-79.442	-0.772
process[Recruitment].ycs_values{1993}	0.000	0.000	-0.871	-71.947	-71.947	0.307
process[Recruitment].ycs_values{1994}	0.000	0.000	-0.102	-72.582	-72.582	-0.285
process[Recruitment].ycs_values{1995}	0.000	0.000	-0.691	-61.908	-61.908	0.373
process[Recruitment].ycs_values{1996}	0.000	0.000	-0.736	-66.552	-66.552	0.074
process[Recruitment].ycs_values{1997}	0.000	0.000	-0.400	-68.176	-68.176	0.416
process[Recruitment].ycs_values{1998}	0.000	0.000	-0.368	-70.707	-70.708	-0.144
process[Recruitment].ycs_values{1999}	0.000	0.000	-0.045	-76.243	-76.243	0.366
process[Recruitment].ycs_values{2000}	0.000	0.000	0.239	-63.330	-63.330	-0.122
process[Recruitment].ycs_values{2001}	0.000	0.000	0.623	-64.995	-64.995	-0.075
process[Recruitment].ycs_values{2002}	0.000	0.000	0.227	-72.280	-72.280	-0.424
process[Recruitment].ycs_values{2003}	0.000	0.000	-0.008	-64.376	-64.376	-0.226
process[Recruitment].ycs_values{2004}	0.000	0.000	-0.260	-67.157	-67.157	-0.985
process[Recruitment].ycs_values{2005}	0.000	0.000	0.321	-62.817	-62.817	-0.618
process[Recruitment].ycs_values{2006}	0.000	0.000	0.123	-69.327	-69.327	-0.865
process[Recruitment].ycs_values{2007}	0.000	0.000	0.042	-54.491	-54.491	-0.760
process[Recruitment].ycs_values{2008}	0.000	0.000	0.503	-61.176	-61.176	-0.738
process[Recruitment].ycs_values{2009}	0.000	0.000	1.010	-48.629	-48.629	-0.072
process[Recruitment].ycs_values{2010}	0.000	0.000	0.674	-51.171	-51.171	0.464
process[Recruitment].ycs_values{2011}	0.000	0.000	1.004	-79.526	-79.526	0.088
process[Recruitment].ycs_values{2012}	0.000	0.000	-0.311	-62.893	-62.893	-0.086
process[Recruitment].ycs_values{2013}	0.000	0.000	1.918	-60.698	-60.698	-0.555
process[Recruitment].ycs_values{2014}	0.000	0.000	0.262	-67.785	-67.785	-0.626

CASAL objective function component values

Component	Base_Model	Sensitivity_1
Tangaroa_bio_autumn	-6.829	-6.834
Tangaroa_bio_summer	-23.880	-23.960
Tangaroa_propn_at_age_aut	175.700	175.800
Tangaroa_propn_at_age_summer	835.900	835.600
longline_Campbell_home_propn_at_age	275.700	275.400
longline_Puysegur_spawn_propn_at_age	363.300	363.300
trawl_observer_propn_at_age	682.600	682.300
prior_on_q[tan_sum].q	-2.364	-2.366
prior_on_q[tan_aut].q	-2.033	-2.037
prior_on_initialization.B0	12.640	12.650
prior_on_natural_mortality.ogive_all	0.000	0.000
prior_on_selectivity[surveysum_sel].male	0.000	0.000
prior_on_selectivity[surveysum_sel].female	0.000	0.000
prior_on_selectivity[surveyaut_sel].male	0.000	0.000
prior_on_selectivity[surveyaut_sel].female	0.000	0.000
prior_on_selectivity[trawl_sel].male	0.000	0.000
prior_on_selectivity[trawl_sel].female	0.000	0.000
prior_on_selectivity[line_home_sel].male	0.000	0.000
prior_on_selectivity[line_home_sel].female	0.000	0.000
prior_on_selectivity[line_spawn_sel].male	0.000	0.000
prior_on_selectivity[line_spawn_sel].female	0.000	0.000
prior_on_recruitment.YCS	-14.440	-14.370
clp1	0.000	0.000
clp2	0.000	0.000
clp3	0.000	0.000
YCS_average_1	0.908	0.904
Total	2297.000	2296.000

Casal2 objective function component values

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
observation->summerTANbiomass-1992	-1.693	-1.693	-1.679	-1.631	-1.631	-1.678
observation->summerTANbiomass-1993	-1.353	-1.353	-1.331	-1.221	-1.221	-1.318
observation->summerTANbiomass-1994	-0.975	-0.975	-0.991	-1.091	-1.091	-1.012
observation->summerTANbiomass-2001	0.430	0.430	0.354	0.273	0.273	0.411
observation->summerTANbiomass-2002	-1.778	-1.778	-1.786	-1.787	-1.787	-1.778
observation->summerTANbiomass-2003	-1.685	-1.685	-1.693	-1.688	-1.688	-1.683
observation->summerTANbiomass-2004	-1.598	-1.598	-1.586	-1.600	-1.600	-1.604
observation->summerTANbiomass-2005	-1.657	-1.657	-1.656	-1.658	-1.658	-1.658
observation->summerTANbiomass-2006	-1.143	-1.143	-1.153	-1.179	-1.179	-1.165
observation->summerTANbiomass-2007	-1.162	-1.162	-1.180	-1.211	-1.211	-1.182
observation->summerTANbiomass-2008	-1.568	-1.568	-1.553	-1.513	-1.513	-1.553
observation->summerTANbiomass-2009	-1.700	-1.700	-1.705	-1.715	-1.715	-1.704
observation->summerTANbiomass-2010	-1.672	-1.672	-1.678	-1.698	-1.698	-1.675
observation->summerTANbiomass-2012	-1.554	-1.554	-1.558	-1.596	-1.596	-1.552
observation->summerTANbiomass-2013	-1.669	-1.669	-1.667	-1.634	-1.634	-1.671
observation->summerTANbiomass-2015	-1.582	-1.582	-1.570	-1.416	-1.416	-1.591
observation->summerTANbiomass-2017	-1.526	-1.526	-1.528	-1.517	-1.517	-1.526
observation->Tangaroa_propn_at_age_summer-1990	44.218	44.218	44.393	44.200	44.200	44.252
observation->Tangaroa_propn_at_age_summer-1992	51.993	51.993	51.753	52.283	52.283	52.033
observation->Tangaroa_propn_at_age_summer-1993	50.200	50.200	50.168	50.265	50.265	50.218
observation->Tangaroa_propn_at_age_summer-1994	49.743	49.743	49.785	49.782	49.782	49.708
observation->Tangaroa_propn_at_age_summer-2001	48.355	48.355	48.237	48.568	48.568	48.471
observation->Tangaroa_propn_at_age_summer-2002	47.830	47.830	47.879	48.038	48.038	47.817
observation->Tangaroa_propn_at_age_summer-2003	48.442	48.442	48.620	48.412	48.412	48.392
observation->Tangaroa_propn_at_age_summer-2004	44.823	44.823	44.865	44.903	44.903	44.825
observation->Tangaroa_propn_at_age_summer-2005	43.097	43.097	43.117	43.060	43.060	43.126
observation->Tangaroa_propn_at_age_summer-2006	43.891	43.891	44.058	43.942	43.942	43.859
observation->Tangaroa_propn_at_age_summer-2007	41.848	41.848	41.841	41.824	41.824	41.858
observation->Tangaroa_propn_at_age_summer-2008	45.225	45.225	45.267	45.127	45.127	45.217
observation->Tangaroa_propn_at_age_summer-2009	46.844	46.844	46.806	46.994	46.994	46.806
observation->Tangaroa_propn_at_age_summer-2010	47.128	47.128	47.202	47.196	47.196	47.192
observation->Tangaroa_propn_at_age_summer-2012	44.353	44.353	44.183	44.772	44.772	44.409
observation->Tangaroa_propn_at_age_summer-2013	47.251	47.251	47.021	47.416	47.416	47.262
observation->Tangaroa_propn_at_age_summer-2015	46.473	46.473	46.342	46.718	46.718	46.475
observation->Tangaroa_propn_at_age_summer-2017	44.182	44.182	44.082	44.204	44.204	44.191
observation->autumnTANbiomass-1992	-1.558	-1.558	-1.572	-1.570	-1.570	-1.559
observation->autumnTANbiomass-1993	-1.741	-1.741	-1.733	-1.726	-1.726	-1.738
observation->autumnTANbiomass-1996	-1.779	-1.779	-1.779	-1.778	-1.778	-1.778
observation->autumnTANbiomass-1998	-1.750	-1.750	-1.750	-1.750	-1.750	-1.750
observation->Tangaroa_propn_at_age_autumn-1992	44.589	44.589	44.443	44.805	44.805	44.577
observation->Tangaroa_propn_at_age_autumn-1993	45.484	45.484	45.443	45.684	45.684	45.494
observation->Tangaroa_propn_at_age_autumn-1996	42.184	42.184	42.295	42.483	42.483	42.185
observation->Tangaroa_propn_at_age_autumn-1998	43.464	43.464	43.610	43.225	43.225	43.468
observation->trawl_propn_at_age-1992	36.067	36.067	35.944	36.594	36.594	36.013
observation->trawl_propn_at_age-1993	27.516	27.516	27.476	27.571	27.571	27.512
observation->trawl_propn_at_age-1994	25.819	25.819	25.764	25.964	25.964	25.768
observation->trawl_propn_at_age-1996	28.394	28.394	28.397	28.617	28.617	28.441
observation->trawl_propn_at_age-1998	24.915	24.915	24.910	25.032	25.032	24.920
observation->trawl_propn_at_age-2001	24.580	24.580	24.542	24.685	24.685	24.563
observation->trawl_propn_at_age-2002	26.770	26.770	26.792	26.936	26.936	26.779
observation->trawl_propn_at_age-2003	34.564	34.564	34.511	34.570	34.570	34.586
observation->trawl_propn_at_age-2004	29.608	29.608	29.608	29.604	29.604	29.505
observation->trawl_propn_at_age-2005	30.147	30.147	30.166	30.267	30.267	30.125
observation->trawl_propn_at_age-2006	33.629	33.629	33.714	33.729	33.729	33.593
observation->trawl_propn_at_age-2007	26.635	26.635	26.588	26.662	26.662	26.617
observation->trawl_propn_at_age-2008	27.059	27.059	27.076	27.053	27.053	27.077
observation->trawl_propn_at_age-2009	37.213	37.213	37.237	37.210	37.210	37.217
observation->trawl_propn_at_age-2010	30.648	30.648	30.694	30.594	30.594	30.722
observation->trawl_propn_at_age-2011	31.266	31.266	31.260	31.339	31.339	31.245
observation->trawl_propn_at_age-2012	32.325	32.325	32.366	32.237	32.237	32.363
observation->trawl_propn_at_age-2013	37.072	37.072	36.943	36.843	36.843	36.957
observation->trawl_propn_at_age-2014	30.640	30.640	30.642	30.576	30.576	30.632
observation->trawl_propn_at_age-2015	33.456	33.456	33.474	33.327	33.327	33.491
observation->trawl_propn_at_age-2016	36.532	36.532	36.482	36.368	36.368	36.534
observation->trawl_propn_at_age-2017	37.755	37.755	37.708	37.641	37.641	37.795
observation->longline_Campbell_home_propn_at_age-1999	45.348	45.348	45.256	45.143	45.143	45.309
observation->longline_Campbell_home_propn_at_age-2001	31.965	31.965	31.950	31.934	31.934	31.984
observation->longline_Campbell_home_propn_at_age-2003	28.644	28.644	28.675	28.610	28.610	28.677
observation->longline_Campbell_home_propn_at_age-2005	32.750	32.750	32.776	32.826	32.826	32.749
observation->longline_Campbell_home_propn_at_age-2009	26.033	26.033	25.611	25.886	25.886	25.939
observation->longline_Campbell_home_propn_at_age-2010	24.302	24.302	24.461	24.338	24.338	24.326
observation->longline_Campbell_home_propn_at_age-2011	28.878	28.878	28.935	28.747	28.747	28.882
observation->longline_Campbell_home_propn_at_age-2012	32.258	32.258	32.389	32.249	32.249	32.279
observation->longline_Campbell_home_propn_at_age-2014	25.495	25.495	25.357	25.391	25.391	25.451
observation->longline_Puyseger_home_propn_at_age-2000	42.745	42.745	42.680	42.956	42.956	43.129
observation->longline_Puyseger_home_propn_at_age-2001	31.770	31.770	31.900	31.791	31.791	31.977
observation->longline_Puyseger_home_propn_at_age-2002	39.978	39.978	39.998	40.179	40.179	40.361
observation->longline_Puyseger_home_propn_at_age-2003	43.527	43.527	43.511	43.694	43.694	43.560
observation->longline_Puyseger_home_propn_at_age-2004	39.957	39.957	40.015	40.076	40.076	40.140
observation->longline_Puyseger_home_propn_at_age-2005	25.532	25.532	25.358	25.506	25.506	25.482
observation->longline_Puyseger_home_propn_at_age-2006	35.210	35.210	35.426	35.107	35.107	35.010
observation->longline_Puyseger_home_propn_at_age-2007	33.981	33.981	33.782	34.137	34.137	34.361
observation->longline_Puyseger_home_propn_at_age-2008	19.139	19.139	19.113	19.090	19.090	19.135
observation->longline_Puyseger_home_propn_at_age-2010	24.238	24.238	24.366	24.038	24.038	23.920
observation->longline_Puyseger_home_propn_at_age-2017	27.200	27.200	27.093	27.441	27.441	27.656
prior->B0->process[Recruitment].b0	12.640	12.640	12.646	12.492	12.492	12.587
prior->summerTANq->catchability[summerTANq].q	-2.363	-2.363	-2.365	-2.240	-2.240	-2.318
prior->autumnTANq->catchability[autumnTANq].q	-2.035	-2.035	-2.037	-1.786	-1.786	-1.939
prior->M_all_x0->selectivity[M_all].x0	0.000	0.000	0.000	0.000	0.000	0.000
prior->M_all_y0->selectivity[M_all].y0	0.000	0.000	0.000	0.000	0.000	0.000
prior->M_all_y1->selectivity[M_all].y1	0.000	0.000	0.000	0.000	0.000	0.000
prior->M_all_y2->selectivity[M_all].y2	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].mu	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].sigma_l	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].sigma_r	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_f].mu	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_f].sigma_l	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_f].sigma_r	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->process[Recruitment].ycs_values{1972}	-0.378	-0.378	-0.365	-0.008	-0.008	-0.368
prior->process[Recruitment].ycs_values{1973}	-0.360	-0.360	-0.349	1.324	1.324	-0.348
prior->process[Recruitment].ycs_values{1974}	-0.397	-0.397	-0.398	0.594	0.594	-0.399
prior->process[Recruitment].ycs_values{1975}	-0.398	-0.398	-0.398	0.143	0.143	-0.398
prior->process[Recruitment].ycs_values{1976}	-0.380	-0.380	-0.383	-0.361	-0.361	-0.375
prior->process[Recruitment].ycs_values{1977}	-0.399	-0.399	-0.398	0.230	0.230	-0.399
prior->process[Recruitment].ycs_values{1978}	-0.398	-0.398	-0.396	-0.122	-0.122	-0.398
prior->process[Recruitment].ycs_values{1979}	-0.335	-0.335	-0.316	0.462	0.462	-0.330
prior->process[Recruitment].ycs_values{1980}	-0.380	-0.380	-0.372	0.017	0.017	-0.379
prior->process[Recruitment].ycs_values{1981}	-0.231	-0.231	-0.213	0.696	0.696	-0.225
prior->process[Recruitment].ycs_values{1982}	-0.364	-0.364	-0.367	-0.206	-0.206	-0.364
prior->process[Recruitment].ycs_values{1983}	-0.326	-0.326	-0.319	0.396	0.396	-0.318
prior->process[Recruitment].ycs_values{1984}	-0.291	-0.291	-0.292	-0.343	-0.343	-0.297
prior->process[Recruitment].ycs_values{1985}	-0.394	-0.394	-0.393	-0.095	-0.095	-0.395
prior->process[Recruitment].ycs_values{1986}	-0.114	-0.114	-0.117	-0.373	-0.373	-0.132
prior->process[Recruitment].ycs_values{1987}	-0.135	-0.135	-0.134	-0.371	-0.371	-0.146
prior->process[Recruitment].ycs_values{1988}	-0.334	-0.334	-0.334	-0.326	-0.326	-0.341
prior->process[Recruitment].ycs_values{1989}	-0.375	-0.375	-0.372	-0.167	-0.167	-0.378
prior->process[Recruitment].ycs_values{1990}	-0.350	-0.350	-0.350	-0.186	-0.186	-0.356
prior->process[Recruitment].ycs_values{1991}	-0.384	-0.384	-0.385	-0.183	-0.183	-0.385
prior->process[Recruitment].ycs_values{1992}	-0.367	-0.367	-0.369	-0.171	-0.171	-0.370
prior->process[Recruitment].ycs_values{1993}	-0.225	-0.225	-0.217	0.650	0.650	-0.228
prior->process[Recruitment].ycs_values{1994}	-0.233	-0.233	-0.232	0.639	0.639	-0.230
prior->process[Recruitment].ycs_values{1995}	-0.192	-0.192	-0.185	0.590	0.590	-0.196
prior->process[Recruitment].ycs_values{1996}	-0.319	-0.319	-0.315	0.329	0.329	-0.320
prior->process[Recruitment].ycs_values{1997}	-0.399	-0.399	-0.399	-0.055	-0.055	-0.399
prior->process[Recruitment].ycs_values{1998}	-0.372	-0.372	-0.373	-0.209	-0.209	-0.373
prior->process[Recruitment].ycs_values{1999}	-0.360	-0.360	-0.360	-0.207	-0.207	-0.358
prior->process[Recruitment].ycs_values{2000}	-0.399	-0.399	-0.399	-0.084	-0.084	-0.399
prior->process[Recruitment].ycs_values{2001}	-0.399	-0.399	-0.399	-0.094	-0.094	-0.399
prior->process[Recruitment].ycs_values{2002}	-0.378	-0.378	-0.377	-0.182	-0.182	-0.380
prior->process[Recruitment].ycs_values{2003}	-0.399	-0.399	-0.399	-0.089	-0.089	-0.399
prior->process[Recruitment].ycs_values{2004}	-0.383	-0.383	-0.383	0.090	0.090	-0.381
prior->process[Recruitment].ycs_values{2005}	-0.249	-0.249	-0.251	0.472	0.472	-0.243
prior->process[Recruitment].ycs_values{2006}	-0.375	-0.375	-0.375	0.155	0.155	-0.372
prior->process[Recruitment].ycs_values{2007}	-0.252	-0.252	-0.253	0.358	0.358	-0.246
prior->process[Recruitment].ycs_values{2008}	-0.368	-0.368	-0.370	0.104	0.104	-0.365
prior->process[Recruitment].ycs_values{2009}	-0.320	-0.320	-0.326	0.126	0.126	-0.320
prior->process[Recruitment].ycs_values{2010}	-0.362	-0.362	-0.364	0.031	0.031	-0.364
prior->process[Recruitment].ycs_values{2011}	-0.392	-0.392	-0.390	-0.069	-0.069	-0.392
prior->process[Recruitment].ycs_values{2012}	-0.394	-0.394	-0.393	-0.018	-0.018	-0.394
prior->process[Recruitment].ycs_values{2013}	-0.389	-0.389	-0.393	-0.002	-0.002	-0.388
prior->process[Recruitment].ycs_values{2014}	-0.396	-0.396	-0.396	0.000	0.000	-0.395
additional_prior->YCS_average_1	0.908	0.908	0.904	0.006	0.006	0.905
total_negloglike	2296.970	2296.970	2296.140	2317.710	2317.710	2298.450
total_score	2296.970	2296.970	2296.140	2317.710	2317.710	2298.450

## [1] "CASAL base model convergence information"
## [1] "fmm: have converged: t = 0.00198541 f = 2297.19"                                                        
## [2] "Successful convergence in optimise"                                                                     
## [3] "Minimiser achieved convergence after 53 quasi-Newton iterations using 91 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-006"                                                                  
## [2] "fmm: have converged: t = 4.30035e-007 f = 2296.34"                                                        
## [3] "Successful convergence in optimise"                                                                       
## [4] "Minimiser achieved convergence after 188 quasi-Newton iterations using 303 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 4.70876e-07 f = 2296.14"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## [1] "[IMPORTANT] FMM: Small step size convergence"
## [2] "FMM: Small step size convergence"

## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
##                        parameter estimate lower.bound upper.bound
## 1 selectivity[trawl_sel].male[3]      200           1         200
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [2] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## [1] ""

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others…

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.7359 0.9329"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.9871 0.9823"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"